We have separate Permanent connector to program EPCQ64ASI16N through Download cable and a separate JTAG connector to load configuration.
Is this possible to configure Cyclone IV FPGA and EPCQ64ASI16N together with single connector?
Yes, it is possible to have single connector.
You can remove Permanent JTAG connector that connected to Serial communication (top JTAG from you Picture).
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